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The Czech dominated early on in the match and then withstood a comeback attempt by the third seed to earn a 6-1 6-4 2-6 6-4 win.
The world number seven, who wrapped up the victory over Ferrer in three hours and four minutes, will play the winner of Tuesday's late quarter-final between three-time defending champion Novak Djokovic and Stanislas Wawrinka.
Berdych clinched the match on his second match point when Ferrer's return of serve went wide. The 2010 Wimbledon finalist has now reached the last four of every major tournament, breaking a sequence of three consecutive quarter-final defeats at Melbourne Park.
Berdych has now won three of his last five matches against Ferrer, a long-time top-five contender.